[Documentation] Transfer all PHB documentation to GitHub (#605)

* initial documentation drafting * empty files for everything, additional formatting for tables * all data import and export docs completed * finish data import, phylogenetic placement, public data sharing * work on phylogenetic construction * progress in phylogenetic construction * finish phylogenetics * add a readme * work on characterization * theiacov text done * finish theiacov, start theiaprok * finish transfer * make gh workflow to build docs * correct broken links, add --force to yml * try manually adding git committer info * do an && instead? * third times the charm * standardizing formatting * standardize definitions * bold! * update ci * try again * add latest version warning; new workflow for version releases; change it to be a main version * add alias labels? may remove * remove update aliases * add code style guide * point version release docs to the actual version release * rename * update so only changes to main are being rendered * organize * remove branch * update readme to go to new link * add (development) next to main * make alias * bye bye attempt * remove extra | * fix issue with table columns * organize the assets folder to a more intuitive structure * add sops and format the getting starteds * remake v2.2.0 and everything else * remove the extra stuff from the GHA so that it works in the future as we desire * change warning so it doesn't mess up when changing versions * update * okay now it's ready to merge
theiagen · Sep 11, 2024 · 6d44d5f · 6d44d5f
1 parent 5be3433
commit 6d44d5f
Show file tree

Hide file tree

Showing 121 changed files with 10,150 additions and 7 deletions.
diff --git a/.github/workflows/build-documentation.yml b/.github/workflows/build-documentation.yml
@@ -0,0 +1,38 @@
+name: build-documentation
+on:
+  push:
+    branches:
+      - main
+
+permissions: 
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - name: Cache dependencies
+        uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs-material mkdocs-material-extensions mkdocs-git-revision-date-localized-plugin mike mkdocs-glightbox
+      
+      - name: Build documentation
+        run: |
+          git config user.name sage-wright
+          git config user.email [email protected] 
+          mike deploy --push main
diff --git a/.github/workflows/build-version-release.yml b/.github/workflows/build-version-release.yml
@@ -0,0 +1,39 @@
+name: version-documentation
+on:
+ release:
+   types: [published]
+
+permissions: 
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - name: Cache dependencies
+        uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs-material mkdocs-material-extensions mkdocs-git-revision-date-localized-plugin mike mkdocs-glightbox
+      
+      - name: Build documentation
+        run: |
+          git config user.name sage-wright
+          git config user.email [email protected] 
+          LATEST_RELEASE=$(curl -sL https://api.github.com/repos/theiagen/public_health_bioinformatics/releases/latest | jq -r ".tag_name")
+          mike deploy --push --update-aliases ${LATEST_RELEASE} latest
+          mike set-default --push latest
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ The Public Health Bioinformatics Bioinformatics repository contains workflows fo
 
 ## Introduction
 
-**More information about the steps undertaken in these workflows is available via the [Theiagen Public Resources Documentation](https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566).**
+**More information about the steps undertaken in these workflows is available via the [Theiagen Public Resources Documentation](https://theiagen.github.io/public_health_bioinformatics/latest/).**
 
 Support for running these workflows can be sought by raising a [GitHub issue](https://github.com/theiagen/public_health_bioinformatics/issues/new) or by contacting Theiagen at [email protected].
 
@@ -16,13 +16,13 @@ The PHB repository contains workflows for the characterization, genomic epidemio
 
 All workflows in the PHB repository end with `_PHB` in order to differentiate them from earlier versions and from the original tools they incorporate.
 
-Briefly, the main *genomic characterization* workflows are split by pathogen type:
+Briefly, the main _genomic characterization_  workflows are split by pathogen type:
 
 1. **Viral** (***TheiaCoV*** workflows)
 2. **Bacterial** (***TheiaProk*** workflows)
-3. **Fungal** (***TheiaEuk*** workflows)
+3. **Fungal** (*[**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md)* workflows)
 
-Many more workflows are available, and are documented in detail in the [Theiagen Public Resources Documentation](https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566).
+Many more workflows are available, and are documented in detail in the [Theiagen Public Resources Documentation](https://theiagen.github.io/public_health_bioinformatics/latest/).
 
 ## On the Shoulder of Giants
 
@@ -83,8 +83,8 @@ The authors declare no conflict of interest.
 
 Please cite this paper if publishing work using any workflows:
 
-> Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. “Accelerating Bioinformatics Implementation in Public Health.” Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051.
+> Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. "Accelerating Bioinformatics Implementation in Public Health." Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051.
 
 Alternatively, please cite this paper if using the TheiaEuk workflow:
 
-> Ambrosio, Frank, Michelle Scribner, Sage Wright, James Otieno, Emma Doughty, Andrew Gorzalski, Danielle Siao, et al. 2023. “TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization.” Frontiers in Public Health 11. https://doi.org/10.3389/fpubh.2023.1198213.
+> Ambrosio, Frank, Michelle Scribner, Sage Wright, James Otieno, Emma Doughty, Andrew Gorzalski, Danielle Siao, et al. 2023. "TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization." Frontiers in Public Health 11. https://doi.org/10.3389/fpubh.2023.1198213.
diff --git a/docs/assets/figures/Core_Gene_SNP.png b/docs/assets/figures/Core_Gene_SNP.png
diff --git a/docs/assets/figures/Create_Terra_Table_example1.png b/docs/assets/figures/Create_Terra_Table_example1.png
diff --git a/docs/assets/figures/Create_Terra_Table_example2.png b/docs/assets/figures/Create_Terra_Table_example2.png
diff --git a/docs/assets/figures/Find_Shared_Variants_PHB.png b/docs/assets/figures/Find_Shared_Variants_PHB.png
diff --git a/docs/assets/figures/Freyja_FASTQ.png b/docs/assets/figures/Freyja_FASTQ.png
diff --git a/docs/assets/figures/Freyja_figure2.png b/docs/assets/figures/Freyja_figure2.png
diff --git a/docs/assets/figures/Freyja_figure3.png b/docs/assets/figures/Freyja_figure3.png
diff --git a/docs/assets/figures/Kraken2.png b/docs/assets/figures/Kraken2.png
diff --git a/docs/assets/figures/Lyve_Set.png b/docs/assets/figures/Lyve_Set.png
diff --git a/docs/assets/figures/Snippy_Streamline.png b/docs/assets/figures/Snippy_Streamline.png
diff --git a/docs/assets/figures/Snippy_Streamline_FASTA.png b/docs/assets/figures/Snippy_Streamline_FASTA.png
diff --git a/docs/assets/figures/Snippy_Variants.png b/docs/assets/figures/Snippy_Variants.png
diff --git a/docs/assets/figures/TheiaCoV.png b/docs/assets/figures/TheiaCoV.png
diff --git a/docs/assets/figures/TheiaEuk_Illumina_PE.png b/docs/assets/figures/TheiaEuk_Illumina_PE.png
diff --git a/docs/assets/figures/TheiaMeta_Illumina_PE.png b/docs/assets/figures/TheiaMeta_Illumina_PE.png
diff --git a/docs/assets/figures/TheiaProk.png b/docs/assets/figures/TheiaProk.png
diff --git a/docs/assets/figures/TheiaValidate.png b/docs/assets/figures/TheiaValidate.png
diff --git a/docs/assets/figures/Workflow_Relationships.png b/docs/assets/figures/Workflow_Relationships.png
diff --git a/docs/assets/figures/Workflow_Relationships_dark.png b/docs/assets/figures/Workflow_Relationships_dark.png
diff --git a/docs/assets/figures/basespace_fetch/step1.png b/docs/assets/figures/basespace_fetch/step1.png
diff --git a/docs/assets/figures/basespace_fetch/step10.png b/docs/assets/figures/basespace_fetch/step10.png
diff --git a/docs/assets/figures/basespace_fetch/step11.png b/docs/assets/figures/basespace_fetch/step11.png
diff --git a/docs/assets/figures/basespace_fetch/step2.png b/docs/assets/figures/basespace_fetch/step2.png
diff --git a/docs/assets/figures/basespace_fetch/step3.png b/docs/assets/figures/basespace_fetch/step3.png
diff --git a/docs/assets/figures/basespace_fetch/step4.png b/docs/assets/figures/basespace_fetch/step4.png
diff --git a/docs/assets/figures/basespace_fetch/step5.png b/docs/assets/figures/basespace_fetch/step5.png
diff --git a/docs/assets/figures/basespace_fetch/step6.png b/docs/assets/figures/basespace_fetch/step6.png
diff --git a/docs/assets/figures/basespace_fetch/step7.png b/docs/assets/figures/basespace_fetch/step7.png
diff --git a/docs/assets/figures/basespace_fetch/step8.png b/docs/assets/figures/basespace_fetch/step8.png
diff --git a/docs/assets/figures/basespace_fetch/step9.png b/docs/assets/figures/basespace_fetch/step9.png
diff --git a/docs/assets/figures/example_krona_report.png b/docs/assets/figures/example_krona_report.png
diff --git a/docs/assets/figures/example_phandango_coloring.png b/docs/assets/figures/example_phandango_coloring.png
diff --git a/docs/assets/files/GPSC_README_PopPUNK2.txt b/docs/assets/files/GPSC_README_PopPUNK2.txt
@@ -0,0 +1,37 @@
+GPSC assignment
+
+Install PopPUNK 2.4 as per instructions at PopPUNK documentation and download 
+the GPS reference database and the GPS designation.
+
+Files required to run GPSC assignment using PopPUNK 2.4:
+1. A 2-column tab-delimited file containing sample name and path to the
+   corresponding assembly (no header)
+2. GPS reference database <GPS_v6>
+3. GPS designation <GPS_v6_external_clusters.csv>
+
+output directory name is assigned using --output
+number of threads can be changed using –threads
+
+Run GPSC assignment:
+
+poppunk_assign --db GPS_v6 \
+               --distances GPS_v6/GPS_v6.dists \
+               --query <2-column path to assembly> \
+               --output <GPSC_assignment> \
+               --external-clustering \
+               GPS_v6_external_clusters.csv
+
+Outputs:
+
+_clusters.csv: popPUNK clusters with dataset specific nomenclature
+_external_clusters.csv: GPSC v6 scheme designations
+
+Novel Clusters are assigned NA in the _external_clusters.csv as they have 
+not been defined in the v6 dataset used to designate the GPSCs. Please email: 
+[email protected] to have novel clusters added to the database and a 
+GPSC cluster name assigned after you have checked for low level contamination 
+which may contribute to biased accessory distances.
+
+Merged clusters: Unsampled diversity may represent missing variation linking two 
+clusters. GPSCs are then merged. For example if GPSC23 and GPSC362 merged, the 
+GPSC would be then reported as GPSC23, with a merge history of GPSC23;362.
diff --git a/docs/assets/files/TheiaEuk_qc_check_template.tsv b/docs/assets/files/TheiaEuk_qc_check_template.tsv
@@ -0,0 +1,18 @@
+taxon	num_reads_raw1	num_reads_raw2	num_reads_clean1	num_reads_clean2	est_coverage_raw	est_coverage_clean	combined_mean_q_raw	r1_mean_q_raw	r2_mean_q_raw	combined_mean_readlength_raw	r1_mean_readlength_raw	r2_mean_readlength_raw	combined_mean_q_clean	r1_mean_q_clean	r2_mean_q_clean	combined_mean_readlength_clean	r1_mean_readlength_clean	r2_mean_readlength_clean	assembly_length_min	assembly_length_max	number_contigs	n50_value	quast_gc_percent_min	quast_gc_percent_max	busco_completeness
+Aspergillus_terreus	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	27960000	31840000	1000	10000			95
+Aspergillus_flavus	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	35090000	42930000	1000	10000			95
+Aspergillus_fumigatus	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	27360000	33400000	1000	10000			95
+Candida_albicans	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	11650000	18700000	1000	10000			95
+Candida_auris	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	12100000	14250000	1000	10000	43	47	95
+Candida_glabrata	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	11810000	14520000	1000	10000			95
+Candida_parapsilosis	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	11570000	13330000	1000	10000			95
+Candida_tropicalis	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	14350000	15730000	1000	10000			95
+Clavispora_lusitaniae	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	11910000	12380000	1000	10000			95
+Coccidioides_immitis	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	27470000	28950000	1000	10000			95
+Cryptococcus_gattii_VGI	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	17230000	18370000	1000	10000			95
+Cryptococcus_neoformans	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	17990000	19750000	1000	10000			95
+Fusarium	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	26090000	72920000	1000	10000			95
+Kluyveromyces_marxianus	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	9555000	13340000	1000	10000			95
+Pichia_kudriavzevii	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	72470000	12940000	1000	10000			95
+Yarrowia_lipolytica	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	19720000	21250000	1000	10000			95
+Candida_haemuloni	1000000	1000000	1000000	1000000	30	30	30	30	30	135	135	135	30	30	30	135	135	135	12590000	13310000	1000	10000			95
diff --git a/docs/assets/files/TheiaProk_FASTA_qc_check_template.tsv b/docs/assets/files/TheiaProk_FASTA_qc_check_template.tsv
@@ -0,0 +1,15 @@
+taxon	assembly_length_min	assembly_length_max	number_contigs	n50_value	quast_gc_percent_min	quast_gc_percent_max	busco_completeness	ani_highest_percent	ani_highest_percent_bases_aligned
+Listeria_monocytogenes	2800000	3200000	500	10000			95	92	70
+Escherichia_coli	4900000	6000000	500	10000			95	92	70
+Shigella	4200000	4900000	500	10000			95	92	70
+Salmonella	4400000	5700000	500	10000			95	92	70
+Campylobacter	1400000	2200000	500	10000			95	92	70
+Vibrio_cholerae	3800000	4300000	500	10000			95	92	70
+Vibrio_parahaemolyticus	4900000	5500000	500	10000			95	92	70
+Vibrio_vulnificus	4700000	5300000	500	10000			95	92	70
+Pseudomonas			500	10000			95		
+Streptococcus			500	10000			95		
+Acinetobacter			500	10000			95		
+Mycobacterium			500	10000			95		
+Legionella			500	10000			95		
+Klebsiella			500	10000			95		
diff --git a/docs/assets/files/TheiaProk_Illumina_PE_qc_check_template.tsv b/docs/assets/files/TheiaProk_Illumina_PE_qc_check_template.tsv
@@ -0,0 +1,15 @@
+taxon	num_reads_raw1	num_reads_raw2	num_reads_clean1	num_reads_clean2	est_coverage_raw	est_coverage_clean	combined_mean_q_raw	r1_mean_q_raw	r2_mean_q_raw	combined_mean_readlength_raw	r1_mean_readlength_raw	r2_mean_readlength_raw	combined_mean_q_clean	r1_mean_q_clean	r2_mean_q_clean	combined_mean_readlength_clean	r1_mean_readlength_clean	r2_mean_readlength_clean	assembly_length_min	assembly_length_max	midas_secondary_genus_abundance	number_contigs	n50_value	quast_gc_percent_min	quast_gc_percent_max	busco_completeness	ani_highest_percent	ani_highest_percent_bases_aligned
+Listeria_monocytogenes	100000	100000	100000	100000	20		30			135			30			135			2800000	3200000	0.01						92	70
+Escherichia_coli	100000	100000	100000	100000	40		30			135			30			135			4900000	6000000	0.01						92	70
+Shigella	100000	100000	100000	100000	40		30			135			30			135			4200000	4900000	0.01						92	70
+Salmonella	100000	100000	100000	100000	30		30			135			30			135			4400000	5700000	0.01						92	70
+Campylobacter	100000	100000	100000	100000	20		30			135			30			135			1400000	2200000	0.01						92	70
+Vibrio_cholerae	100000	100000	100000	100000	40		30			135			30			135			3800000	4300000	0.01						92	70
+Vibrio_parahaemolyticus	100000	100000	100000	100000	40		30			135			30			135			4900000	5500000	0.01						92	70
+Vibrio_vulnificus	100000	100000	100000	100000	40		30			135			30			135			4700000	5300000	0.01						92	70
+Pseudomonas	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
+Streptococcus	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
+Acinetobacter	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
+Mycobacterium	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
+Legionella	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
+Klebsiella	100000	100000	100000	100000	30	30	30	30	30	135	135	135	30	30	30	135	135	135				500	10000			95		
diff --git a/docs/assets/files/example_excluded_samples.tsv b/docs/assets/files/example_excluded_samples.tsv
@@ -0,0 +1,10 @@
+Samples excluded for quality thresholds:
+sample_name	message	
+sample2	VADR skipped due to poor assembly
+sample3	VADR number alerts too high: 3 greater than limit of 0
+sample4	Number of Ns was too high: 10000 greater than limit of 5000
+
+Samples excluded for missing required metadata (will have empty values in indicated columns):
+tablename_id	organism	country	library_layout
+sample5			paired
+sample6	SARS-CoV-2	USA
diff --git a/docs/assets/files/theiavalidate/example_exact_differences.tsv b/docs/assets/files/theiavalidate/example_exact_differences.tsv
@@ -0,0 +1,8 @@
+	columnA-string	columnA-string	columnB-set	columnB-set	columnC-ignore	columnC-ignore	columnD-float	columnD-float	columnE-missing	columnE-missing
+	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv
+samples										
+sample1			item1,item2,item3	item1,item3,item2	cheese	cheesecake	1000.0	999.0		
+sample2	option1	option2	item1,item3,item2	item1,item2,item3	cheesecake	batter				
+sample3	option2	option1	item1,item2,item3	item1,item2	cake	cheese	14.0	24.0	present	
+sample4			item2,item1	item1,item2			3492.0	728.0		
+sample5			item1,item2	item1,item2,item3			3.0	4.0		
diff --git a/docs/assets/files/theiavalidate/example_summary.pdf b/docs/assets/files/theiavalidate/example_summary.pdf
diff --git a/docs/assets/files/theiavalidate/example_validation_criteria_differences.tsv b/docs/assets/files/theiavalidate/example_validation_criteria_differences.tsv
@@ -0,0 +1,7 @@
+Column	columnB-set	columnB-set	columnD-float	columnD-float	columnE-missing	columnE-missing
+Table	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv	example_table1.tsv	example_table2.tsv
+sample1						
+sample2						
+sample3	item1,item2,item3	item1,item2	14.0	24.0	present	
+sample4			3492.0	728.0		
+sample5	item1,item2	item1,item2,item3	3.0	4.0		
diff --git a/docs/assets/files/theiavalidate/filtered_example_table1.tsv b/docs/assets/files/theiavalidate/filtered_example_table1.tsv
@@ -0,0 +1,6 @@
+samples	columnA-string	columnB-set	columnC-ignore	columnD-float	columnE-missing
+sample1	option1	item1,item2,item3	cheese	1000	present
+sample2	option1	item1,item3,item2	cheesecake	12	present
+sample3	option2	item1,item2,item3	cake	14	present
+sample4	option1	item2,item1	cakebatter	3492	
+sample5	option2	item1,item2	batter	3	present
diff --git a/docs/assets/files/theiavalidate/filtered_example_table2.tsv b/docs/assets/files/theiavalidate/filtered_example_table2.tsv
@@ -0,0 +1,6 @@
+samples	columnA-string	columnB-set	columnC-ignore	columnD-float	columnE-missing
+sample1	option1	item1,item3,item2	cheesecake	999	present
+sample2	option2	item1,item2,item3	batter	12	present
+sample3	option1	item1,item2	cheese	24	
+sample4	option1	item1,item2	cakebatter	728	
+sample5	option2	item1,item2,item3	batter	4	present
diff --git a/docs/assets/files/theiavalidate/theiacov-validation-criteria.txt b/docs/assets/files/theiavalidate/theiacov-validation-criteria.txt
@@ -0,0 +1,24 @@
+column	criteria
+abricate_flu_subtype	EXACT
+abricate_flu_type	EXACT
+assembly_length_unambiguous	0.01
+assembly_mean_coverage	0.01
+irma_subtype	EXACT
+irma_type	EXACT
+kraken_human	EXACT
+kraken_human_dehosted	EXACT
+kraken_sc2	EXACT
+kraken_sc2_dehosted	EXACT
+kraken_target_org	EXACT
+kraken_target_org_dehosted	EXACT
+nextclade_aa_dels	SET
+nextclade_aa_subs	SET
+nextclade_clade	EXACT
+nextclade_lineage	EXACT
+nextclade_tamiflu_resistance_aa_subs	SET
+num_reads_clean1	EXACT
+num_reads_clean2	EXACT
+number_N	0.01
+pango_lineage	EXACT
+percent_reference_coverage	0.01
+vadr_num_alerts	EXACT
diff --git a/docs/assets/files/theiavalidate/theiaeuk-validation-criteria.txt b/docs/assets/files/theiavalidate/theiaeuk-validation-criteria.txt
@@ -0,0 +1,13 @@
+column	criteria
+assembly_length	0.01
+busco_results	EXACT
+clade_type	EXACT
+est_coverage_clean	0.01
+est_coverage_raw	0.01
+gambit_predicted_taxon	EXACT
+n50_value	0.01
+num_reads_clean1	EXACT
+num_reads_clean2	EXACT
+number_contigs	0.01
+quast_gc_percent	0.01
+theiaeuk_snippy_variants_hits	SET
diff --git a/docs/assets/files/theiavalidate/theiaprok-validation-criteria.txt b/docs/assets/files/theiavalidate/theiaprok-validation-criteria.txt
@@ -0,0 +1,56 @@
+column	criteria
+abricate_abaum_plasmid_type_genes	SET
+agrvate_agr_group	EXACT
+amrfinderplus_amr_core_genes	SET
+amrfinderplus_amr_plus_genes	SET
+amrfinderplus_stress_genes	SET
+amrfinderplus_virulence_genes	SET
+ani_highest_percent	0.01
+ani_top_species_match	EXACT
+assembly_length	0.01
+busco_results	EXACT
+ectyper_predicted_serotype	EXACT
+emmtypingtool_emm_type	EXACT
+est_coverage_clean	0.01
+est_coverage_raw	0.01
+gambit_predicted_taxon	EXACT
+genotyphi_final_genotype	EXACT
+hicap_genes	SET
+hicap_serotype	EXACT
+kaptive_k_type	EXACT
+kleborate_genomic_resistance_mutations	SET
+kleborate_key_resistance_genes	SET
+kleborate_mlst_sequence_type	EXACT
+legsta_predicted_sbt	EXACT
+lissero_serotype	SET
+meningotype_serogroup	EXACT
+midas_primary_genus	EXACT
+midas_secondary_genus	EXACT
+midas_secondary_genus_abundance	0.01
+n50_value	0.01
+ngmaster_ngmast_sequence_type	EXACT
+ngmaster_ngstar_sequence_type	EXACT
+num_reads_clean1	EXACT
+num_reads_clean2	EXACT
+number_contigs	0.01
+pasty_serogroup	EXACT
+pbptyper_predicted_1A_2B_2X	EXACT
+plasmidfinder_plasmids	SET
+poppunk_gps_cluster	EXACT
+seqsero2_predicted_serotype	EXACT
+seroba_ariba_serotype	EXACT
+seroba_serotype	EXACT
+serotypefinder_serotype	EXACT
+shigatyper_ipaB_presence_absence	EXACT
+shigatyper_predicted_serotype	EXACT
+shigeifinder_cluster	EXACT
+shigeifinder_serotype	EXACT
+sistr_predicted_serotype	EXACT
+sonneityping_final_genotype	EXACT
+spatyper_type	EXACT
+srst2_vibrio_serogroup	EXACT
+staphopiasccmec_types_and_mecA_presence	EXACT
+tbprofiler_main_lineage	EXACT
+tbprofiler_resistance_genes	SET
+ts_mlst_predicted_st	EXACT
+virulencefinder_hits	EXACT
diff --git a/docs/assets/logos/Theiagen-Logo-White.png b/docs/assets/logos/Theiagen-Logo-White.png
diff --git a/docs/assets/logos/Theiagen-Symbol-Standard-01.png b/docs/assets/logos/Theiagen-Symbol-Standard-01.png
diff --git a/docs/assets/metadata_formatters/Mercury_Prep_N_Batch_MPXV_Metadata_Formatter_2022_12_23.xlsx b/docs/assets/metadata_formatters/Mercury_Prep_N_Batch_MPXV_Metadata_Formatter_2022_12_23.xlsx
diff --git a/docs/assets/metadata_formatters/Mercury_Prep_N_Batch_SC2_Metadata_Formatter_2023_05_22.xlsx b/docs/assets/metadata_formatters/Mercury_Prep_N_Batch_SC2_Metadata_Formatter_2023_05_22.xlsx
diff --git a/docs/assets/metadata_formatters/Terra_2_NCBI-MICROBE-metadata-2022-07-11.xlsx b/docs/assets/metadata_formatters/Terra_2_NCBI-MICROBE-metadata-2022-07-11.xlsx
diff --git a/docs/assets/metadata_formatters/Terra_2_NCBI-PATHOGEN-metadata-2024-04-30.xlsx b/docs/assets/metadata_formatters/Terra_2_NCBI-PATHOGEN-metadata-2024-04-30.xlsx
diff --git a/docs/assets/metadata_formatters/Terra_2_NCBI-VIRUS-metadata-2022-09-09.xlsx b/docs/assets/metadata_formatters/Terra_2_NCBI-VIRUS-metadata-2022-09-09.xlsx
diff --git a/docs/assets/new_workflow_template.md b/docs/assets/new_workflow_template.md
@@ -0,0 +1,44 @@
+# Workflow Name
+
+## Quick Facts
+
+| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
+|---|---|---|---|---|
+| [Workflow Type](../../workflows_overview/workflows_type.md/#link-to-workflow-type) | [Applicable Kingdom](../../workflows_overview/workflows_kingdom.md/#link-to-applicable-kingdom) | PHB <version with last changes> | <command-line compatibility> | <workflow level on terra> |
+
+## Workflow_Name_On_Terra
+
+Description of the workflow.
+
+### Inputs
+
+| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
+|---|---|---|---|---|---|
+| task_name | **variable_name** | Type | Description | Default Value | Required/Optional |
+
+### Workflow Tasks
+
+Description of the workflow tasks
+
+??? task "`tool_name`: Description of tool"
+    Description of the task
+
+    !!! techdetails "Tool Name Technical Details"
+        |  | Links | 
+        | --- | --- | 
+        | Task | [link to task on GitHub] |
+        | Software Source Code | [link to tool's source code] |
+        | Software Documentation | [link to tool's documentation] |
+        | Original Publication | [link to tool's publication] |
+
+### Outputs
+
+| **Variable** | **Type** | **Description** |
+|---|---|---|
+| variable_name | Type | Description |
+
+## References (if applicable)
+
+> reference1
+<!-- -->
+> reference2
diff --git a/docs/assets/sops/TG-AUGUR-01_Augur_v1.pdf b/docs/assets/sops/TG-AUGUR-01_Augur_v1.pdf
diff --git a/docs/assets/sops/TG-FLU-PE_SOP_Flu_IlluminaPE_v1.pdf b/docs/assets/sops/TG-FLU-PE_SOP_Flu_IlluminaPE_v1.pdf
diff --git a/docs/assets/sops/TG-FREY-01_FreyjaFASTQ_v2.pdf b/docs/assets/sops/TG-FREY-01_FreyjaFASTQ_v2.pdf
diff --git a/docs/assets/sops/TG-FREY-02_FreyjaPlot_v3.pdf b/docs/assets/sops/TG-FREY-02_FreyjaPlot_v3.pdf
diff --git a/docs/assets/sops/TG-FREY-03-SOP_FreyjaDashboard_v2.pdf b/docs/assets/sops/TG-FREY-03-SOP_FreyjaDashboard_v2.pdf
diff --git a/docs/assets/sops/TG-FREY-04_FreyjaUpdate_v2.pdf b/docs/assets/sops/TG-FREY-04_FreyjaUpdate_v2.pdf
diff --git a/docs/assets/sops/TG-GISAID-01_Terra2GISAID_v2.pdf b/docs/assets/sops/TG-GISAID-01_Terra2GISAID_v2.pdf
diff --git a/docs/assets/sops/TG-SC2-CL_SC2_ClearLabs_v3.pdf b/docs/assets/sops/TG-SC2-CL_SC2_ClearLabs_v3.pdf
diff --git a/docs/assets/sops/TG-SC2-FST_Analyzing_SC2_Using_TheiaCoV_FASTA_PHB_v2.pdf b/docs/assets/sops/TG-SC2-FST_Analyzing_SC2_Using_TheiaCoV_FASTA_PHB_v2.pdf
diff --git a/docs/assets/sops/TG-SC2-ONT_Analyzing_SC2_Using_TheiaCov_ONT_PHB_v2.pdf b/docs/assets/sops/TG-SC2-ONT_Analyzing_SC2_Using_TheiaCov_ONT_PHB_v2.pdf
diff --git a/docs/assets/sops/TG-SC2-PE_SC2_TheiaCoV_IlluminaPE_v3.pdf b/docs/assets/sops/TG-SC2-PE_SC2_TheiaCoV_IlluminaPE_v3.pdf
diff --git a/docs/assets/sops/TG-SC2-SE_SC2_TheiaCoV_IlluminaSE_v3.pdf b/docs/assets/sops/TG-SC2-SE_SC2_TheiaCoV_IlluminaSE_v3.pdf
diff --git a/docs/assets/sops/TG-TER-03_GettingStartedInTerra_v3.pdf b/docs/assets/sops/TG-TER-03_GettingStartedInTerra_v3.pdf
diff --git a/docs/assets/sops/TG-TER-04_BaseSpaceFetch_v2.pdf b/docs/assets/sops/TG-TER-04_BaseSpaceFetch_v2.pdf